olgabot/rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

R

Issues

DESeq: Generate code to replot heatmaps for usability and reproducibility
#5 opened 13 years ago by olgabot
0
Add SAMSeq
#11 opened 13 years ago by olgabot
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Add DEXSeq
#10 opened 13 years ago by olgabot
0
DESeq cannot handle large numbers of samples
#9 opened 13 years ago by olgabot
0
PrEC_group2of2 BAM files don't copy correctly
#8 opened 13 years ago by olgabot
3
Check number of groups specified
#4 opened 13 years ago by olgabot
0
Prevent 1-to-1 comparisons
#6 opened 13 years ago by olgabot
0
LNCaP_group1of1 had NO counts when building from scratch
#7 opened 13 years ago by olgabot
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Check for "group" in ID name
#1 opened 13 years ago by olgabot
0
RSeQC: feed strandedness into RPKM counts
#2 opened 13 years ago by olgabot
0
Add "professional" getopts functionality
#3 opened 13 years ago by olgabot
0